Package index • CrossAncestryGenPhen

Main Functions

split_stratified_ancestry_sets(): Split Expression and Metadata into Train, Test, and Inference Sets

perm_interaction_effect(): Simple Permutation-Based Interaction Test (No Bootstrapping, No Convergence)

limma_interaction_effect(): Limma-Based Interaction Test

perm_correlation_difference(): Simple Permutation Test for Correlation Differences

perm_prediction_difference(): Permutation Test for Prediction Performance Differences

param_gls_summary(): Parametric GLS Feature Summary Across Iterations

RP_aggregation(): Aggregate gene statistics using Rank Product

Visualization Functions

plot_feature(): Plot feature distributions across two splits

plot_stratified_sets(): Plot Sample Counts by Stratified Variable and Dataset Split

plot_stratified_feature(): Plot stratified feature distributions across splits

plot_null_distribution(): Plot permutation-based T-statistics with observed values and p-values

plot_pvalue_distribution(): Plot P-value Distribution Colored by a Binned Fill Variable

plot_correlation_heatmap(): ComplexHeatmap of Correlation Matrix Across Iterations

plot_jaccard_heatmap(): Plot Jaccard Heatmap of Sample Reuse Across Iterations

plot_correlation_difference(): Plot correlation differences with optional facets

plot_volcano(): Volcano Plot

plot_pvalue_concordance(): Plot concordance of -log10 p-values between two methods

Utility Functions

track_sample_ids(): Track Sample Roles and IDs from a Split

compute_jaccard_matrix(): Compute Jaccard Similarity Matrix Between Iterations

compute_correlation_matrix(): Compute Correlation Matrix from Long-format Data

Simulation Functions (not yet finished)

inject_DEG_signal(): Inject Simulated DEGs and Interaction Effects into NB Counts

plot_simulated_features(): Plot Simulated Features by Ancestry and Group (base R + data.table)

simulate_NB_counts(): Simulate Negative Binomial RNA-seq Counts from Real Data

TESTING

boot_interaction_effect(): Simple Bootstrap-Based Interaction Estimation with CI Level Control

boot_correlation_diff(): Bootstrap-Based Correlation Difference Test (Unstratified)